Crystal structure of mouse CARM1 in complex with inhibitor SA0678

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 36% strand (DSSP).

Ligands and binding sites

• 6L7 · [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-azaniumylethyl)-[(3~{S})-3-azaniumyl-4-oxidanyl-4-oxidanylidene-butyl]azanium · ligand · 4 copies · chains A, B, C, D
• DXE · 1,2-dimethoxyethane · ligand · 2 copies · chains A, B, C
• M2M · 1-methoxy-2-(2-methoxyethoxy)ethane · ligand · chains A
• EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
• B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, D
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 1858 Ų buried · 25 hydrogen bonds · protein-protein
• C–D · 1824 Ų buried · 27 hydrogen bonds · protein-protein
• B–D · 850 Ų buried · 11 hydrogen bonds · protein-protein
• A–D · 181 Ų buried · 1 hydrogen bond · protein-protein
• B–C · 176 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 5NTC · Crystal structure of mouse CARM1 in complex with inhibitor SA0678 · the same entry in another collection · chain D against D, TM-score 1.00
• Q9WVG6 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q9WVG6) · a predicted model of the same protein · chain D against A, TM-score 0.99

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9WVG6
• Elsewhere: RCSB PDB 5NTC · PDBe 5NTC · UniProt Q9WVG6